Related Experiment Video
Updated: Jul 28, 2026
10:34
Ligand Nano-cluster Arrays in a Supported Lipid Bilayer
Published on: April 23, 2017
SLATE: a method for the superposition of flexible ligands
J E Mills1, I J de Esch, T D Perkins
1Department of Pharmacology, University of Cambridge, UK.
Journal of Computer-Aided Molecular Design
|February 24, 2001
Summary
A new program, SLATE, superimposes flexible molecules using simulated annealing to predict receptor atom positions for drug design. This method aids in understanding ligand-receptor interactions for multiple targets.
Area of Science:
- Computational chemistry
- Structural biology
- Drug discovery
Background:
- Superimposing flexible molecules is crucial for understanding drug-receptor interactions.
- Accurate prediction of ligand binding poses aids in rational drug design.
Purpose of the Study:
- To introduce SLATE, a novel program for flexible molecule superposition.
- To develop a method for predicting receptor atom positions involved in hydrogen bonding with multiple ligands.
Main Methods:
- SLATE utilizes simulated annealing to minimize differences in distance matrices based on hydrogen-bonding and aromatic ring properties.
- A molecular stacking method is employed, using multiple pairwise matches.
- The DOH program uses these molecular stacks to predict receptor atom positions.
Main Results:
- The methodology was successfully applied to various targets, including dihydrofolate reductase, thermolysin, H3 histamine receptors, alpha2 adrenoceptors, and 5-HT1D receptors.
- The prediction of receptor-atom positions is feasible when sufficient and diverse molecular data is available.
Conclusions:
- SLATE provides a novel approach for flexible molecule superposition.
- The developed methodology enables the prediction of key receptor-ligand interaction points, applicable to compound design and optimization.
Related Concept Videos
02:51Metal-Ligand Bonds
The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
02:58Crystal Field Theory - Octahedral Complexes
Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
02:40Ligand Binding Sites
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
00:49Ligand Binding and Linkage
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
00:43Complexometric Titration: Ligands
Different monodentate and polydentate ligands are used as complexing agents in complexometric titration reactions. The formation of complexes by mono- and bidentate ligands involves two or more intermediate steps, limiting their use as complexing agents. In comparison, polydentate ligands can form complexes with metal ions in a single-step process, facilitating sharper end points. This means polydentate ligands, such as amino carboxylic acid derivatives, are most commonly employed in...